Abstract
The identification of signals of very recent positive selection provides information about the adaptation of modern humans to local conditions. We report here on a genome-wide scan for signals of very recent positive selection in favor of variants that have not yet reached fixation. We describe a new analytical method for scanning single nucleotide polymorphism (SNP) data for signals of recent selection, and apply this to data from the International HapMap Project. In all three continental groups we find widespread signals of recent positive selection. Most signals are region-specific, though a significant excess are shared across groups. Contrary to some earlier low resolution studies that suggested a paucity of recent selection in sub-Saharan Africans, we find that by some measures our strongest signals of selection are from the Yoruba population. Finally, since these signals indicate the existence of genetic variants that have substantially different fitnesses, they must indicate loci that are the source of significant phenotypic variation. Though the relevant phenotypes are generally not known, such loci should be of particular interest in mapping studies of complex traits. For this purpose we have developed a set of SNPs that can be used to tag the strongest ∼250 signals of recent selection in each population.
Highlights
The evolution of modern human populations has been accompanied by dramatic changes in environment and lifestyle
In order to pursue this type of signal for genome-wide single nucleotide polymorphism (SNP) data, we have developed a new test statistic that we denote integrated haplotype score (iHS)
In simulations we find that high frequency selected sites tend to have both strongly negative iHS scores and strongly negative values of Fay and Wu’s H test [37] for ascertained SNPs (Hasc)
Summary
The evolution of modern human populations has been accompanied by dramatic changes in environment and lifestyle. In the last 100,000 years, behaviorally modern humans have spread from Africa to colonize most of the globe. Further dramatic changes occurred with the transition from hunter-gatherer to agricultural societies, starting about 10,000–12,000 years ago in the Fertile Crescent, and a little later elsewhere. This was a period marked by rapid increases in human population densities. Increased population density promoted the spread of infectious diseases, as did the new proximity of farmers to animal pathogens [1,2]
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